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Yoo W, Shealy NG, Zieba JK, Torres TP, Baltagulov M, Thomas JD, Shelton CD, McGovern AG, Foegeding NJ, Olsan EE, Byndloss MX. Salmonella Typhimurium expansion in the inflamed murine gut is dependent on aspartate derived from ROS-mediated microbiota lysis. Cell Host Microbe 2024; 32:887-899.e6. [PMID: 38806059 PMCID: PMC11189616 DOI: 10.1016/j.chom.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/20/2024] [Accepted: 05/01/2024] [Indexed: 05/30/2024]
Abstract
Inflammation boosts the availability of electron acceptors in the intestinal lumen, creating a favorable niche for pathogenic Enterobacteriaceae. However, the mechanisms linking intestinal inflammation-mediated changes in luminal metabolites and pathogen expansion remain unclear. Here, we show that mucosal inflammation induced by Salmonella enterica serovar Typhimurium (S. Tm) infection increases intestinal levels of the amino acid aspartate. S. Tm used aspartate-ammonia lyase (aspA)-dependent fumarate respiration for growth in the murine gut only during inflammation. AspA-dependent growth advantage was abolished in the gut of germ-free mice and restored in gnotobiotic mice colonized with members of the classes Bacteroidia and Clostridia. Reactive oxygen species (ROS) produced during the host response caused lysis of commensal microbes, resulting in the release of microbiota-derived aspartate that was used by S. Tm, in concert with nitrate-dependent anaerobic respiration, to outcompete commensal Enterobacteriaceae. Our findings demonstrate the role of microbiota-derived amino acids in driving respiration-dependent S. Tm expansion during colitis.
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Affiliation(s)
- Woongjae Yoo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Nicolas G Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jacob K Zieba
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Teresa P Torres
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madi Baltagulov
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julia D Thomas
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Catherine D Shelton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Anna G McGovern
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nora J Foegeding
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Erin E Olsan
- Department of Biological Sciences, California State University, Sacramento, CA 95819, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Digestive Disease Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, TN 37235, USA; Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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2
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Glenn SJ, Gentry-Lear Z, Shavlik M, Harms MJ, Asaki TJ, Baylink A. Bacterial vampirism mediated through taxis to serum. eLife 2024; 12:RP93178. [PMID: 38820052 PMCID: PMC11142651 DOI: 10.7554/elife.93178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024] Open
Abstract
Bacteria of the family Enterobacteriaceae are associated with gastrointestinal (GI) bleeding and bacteremia and are a leading cause of death, from sepsis, for individuals with inflammatory bowel diseases. The bacterial behaviors and mechanisms underlying why these bacteria are prone to bloodstream entry remain poorly understood. Herein, we report that clinical isolates of non-typhoidal Salmonella enterica serovars, Escherichia coli, and Citrobacter koseri are rapidly attracted toward sources of human serum. To simulate GI bleeding, we utilized an injection-based microfluidics device and found that femtoliter volumes of human serum are sufficient to induce bacterial attraction to the serum source. This response is orchestrated through chemotaxis and the chemoattractant L-serine, an amino acid abundant in serum that is recognized through direct binding by the chemoreceptor Tsr. We report the first crystal structures of Salmonella Typhimurium Tsr in complex with L-serine and identify a conserved amino acid recognition motif for L-serine shared among Tsr orthologues. We find Tsr to be widely conserved among Enterobacteriaceae and numerous World Health Organization priority pathogens associated with bloodstream infections. Lastly, we find that Enterobacteriaceae use human serum as a source of nutrients for growth and that chemotaxis and the chemoreceptor Tsr provide a competitive advantage for migration into enterohemorrhagic lesions. We define this bacterial behavior of taxis toward serum, colonization of hemorrhagic lesions, and the consumption of serum nutrients as 'bacterial vampirism', which may relate to the proclivity of Enterobacteriaceae for bloodstream infections.
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Affiliation(s)
- Siena J Glenn
- Washington State University, Department of Veterinary Microbiology and PathologyPullmanUnited States
| | | | - Michael Shavlik
- University of Oregon, Institute of Molecular BiologyEugeneUnited States
| | - Michael J Harms
- University of Oregon, Institute of Molecular BiologyEugeneUnited States
- University of Oregon, Department of Chemistry & BiochemistryEugeneUnited States
| | - Thomas J Asaki
- Washington State University, Department of Mathematics and StatisticsPullmanUnited States
| | - Arden Baylink
- Washington State University, Department of Veterinary Microbiology and PathologyPullmanUnited States
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3
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Doranga S, Conway T. Nitrogen assimilation by E. coli in the mammalian intestine. mBio 2024; 15:e0002524. [PMID: 38380942 PMCID: PMC10936423 DOI: 10.1128/mbio.00025-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Nitrogen is an essential element for all living organisms, including Escherichia coli. Potential nitrogen sources are abundant in the intestine, but knowledge of those used specifically by E. coli to colonize remains limited. Here, we sought to determine the specific nitrogen sources used by E. coli to colonize the streptomycin-treated mouse intestine. We began by investigating whether nitrogen is limiting in the intestine. The NtrBC two-component system upregulates approximately 100 genes in response to nitrogen limitation. We showed that NtrBC is crucial for E. coli colonization, although most genes of the NtrBC regulon are not induced, which indicates that nitrogen is not limiting in the intestine. RNA-seq identified upregulated genes in colonized E. coli involved in transport and catabolism of seven amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine. Competitive colonization experiments revealed that L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides serve as nitrogen sources for E. coli in the intestine. Furthermore, the colonization defect of a L-serine deaminase mutant was rescued by excess nitrogen in the drinking water but not by an excess of carbon and energy, demonstrating that L-serine serves primarily as a nitrogen source. Similar rescue experiments showed that N-acetylneuraminic acid serves as both a carbon and nitrogen source. To a minor extent, aspartate and ammonia also serve as nitrogen sources. Overall, these findings demonstrate that E. coli utilizes multiple nitrogen sources for successful colonization of the mouse intestine, the most important of which is L-serine. IMPORTANCE While much is known about the carbon and energy sources that are used by E. coli to colonize the mammalian intestine, very little is known about the sources of nitrogen. Interrogation of colonized E. coli by RNA-seq revealed that nitrogen is not limiting, indicating an abundance of nitrogen sources in the intestine. Pathways for assimilation of nitrogen from several amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine were induced in mice. Competitive colonization assays confirmed that mutants lacking catabolic pathways for L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides had colonization defects. Rescue experiments in mice showed that L-serine serves primarily as a nitrogen source, whereas N-acetylneuraminic acid provides both carbon and nitrogen. Of the many nitrogen assimilation mutants tested, the largest colonization defect was for an L-serine deaminase mutant, which demonstrates L-serine is the most important nitrogen source for colonized E. coli.
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Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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4
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Sugihara K, Kamada N. Metabolic network of the gut microbiota in inflammatory bowel disease. Inflamm Regen 2024; 44:11. [PMID: 38443988 PMCID: PMC10913301 DOI: 10.1186/s41232-024-00321-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Gut dysbiosis is closely linked to the pathogenesis of inflammatory bowel disease (IBD). Emerging studies highlight the relationship between host metabolism and the modulation of gut microbiota composition through regulating the luminal microenvironment. In IBD, various disease-associated factors contribute to the significant perturbation of host metabolism. Such disturbance catalyzes the selective proliferation of specific microbial populations, particularly pathobionts such as adherent invasive Escherichia coli and oral-derived bacteria. Pathobionts employ various strategies to adapt better to the disease-associated luminal environments. In addition to the host-microbe interaction, recent studies demonstrate that the metabolic network between commensal symbionts and pathobionts facilitates the expansion of pathobionts in the inflamed gut. Understanding the metabolic network among the host, commensal symbionts, and pathobionts provides new insights into the pathogenesis of IBD and novel avenues for treating IBD.
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Affiliation(s)
- Kohei Sugihara
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Nobuhiko Kamada
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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5
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Bai JDK, Saha S, Wood M, Chen B, Li J, Dow LE, Montrose DC. Serine Supports Epithelial and Immune Cell Function in Colitis. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00071-3. [PMID: 38417696 DOI: 10.1016/j.ajpath.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/28/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders of the gastrointestinal tract that are largely driven by immune cell activity; mucosal healing is critical for remission. Serine is a nonessential amino acid that supports epithelial and immune cell metabolism and proliferation; however, whether these roles affect IBD pathogenesis is not well understood. Here, we show that serine synthesis increases selectively in the epithelial cells of colons from patients with IBD and murine models of colitis. Inhibiting serine synthesis impairs colonic mucosal healing and increases susceptibility to acute injury in mice, effects associated with impaired epithelial cell proliferation. Dietary removal of serine similarly sensitizes mice to acute chemically induced colitis but ameliorates inflammation in chronic colitis models. The anti-inflammatory effect of exogenous serine depletion in chronic colitis is associated with mitochondrial dysfunction of macrophages, resulting in impaired nucleotide production and proliferation. Collectively, these results suggest that serine plays an important role in both epithelial and immune cell biology in the colon and that modulating its availability could affect IBD pathogenesis.
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Affiliation(s)
- Ji Dong K Bai
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York
| | - Suchandrima Saha
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York
| | - Michael Wood
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York
| | - Bo Chen
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York; Stony Brook Cancer Center, Stony Brook, New York
| | - Jinyu Li
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York
| | - Lukas E Dow
- Department of Medicine, Weill Cornell Medicine, New York, New York; Department of Biochemistry, Weill Cornell Medicine, New York, New York
| | - David C Montrose
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York; Stony Brook Cancer Center, Stony Brook, New York.
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6
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Moreira de Gouveia MI, Bernalier-Donadille A, Jubelin G. Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease. BIOLOGY 2024; 13:142. [PMID: 38534413 DOI: 10.3390/biology13030142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom.
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Affiliation(s)
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000 Clermont-Ferrand, France
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Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C. Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics. Microbiol Spectr 2024; 12:e0114423. [PMID: 38230938 PMCID: PMC10846184 DOI: 10.1128/spectrum.01144-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member Caenorhabditis elegans microbiome community comprising the immune-protective target species Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.IMPORTANCEWhile various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm Caenorhabditis elegans comprising the host-beneficial Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11 in vitro and in vivo. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Inga K. Hamerich
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Reena Debray
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nancy Obeng
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Nutriinformatics, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
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8
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Tearle JLE, Tang A, Vasanthakumar A, James KR. Role reversals: non-canonical roles for immune and non-immune cells in the gut. Mucosal Immunol 2024; 17:137-146. [PMID: 37967720 DOI: 10.1016/j.mucimm.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The intestine is home to an intertwined network of epithelial, immune, and neuronal cells as well as the microbiome, with implications for immunity, systemic metabolism, and behavior. While the complexity of this microenvironment has long since been acknowledged, recent technological advances have propelled our understanding to an unprecedented level. Notably, the microbiota and non-immune or structural cells have emerged as important conductors of intestinal immunity, and by contrast, cells of both the innate and adaptive immune systems have demonstrated non-canonical roles in tissue repair and metabolism. This review highlights recent works in the following two streams: non-immune cells of the intestine performing immunological functions; and traditional immune cells exhibiting non-immune functions in the gut.
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Affiliation(s)
- Jacqueline L E Tearle
- Garvan Institute of Medical Research, Darlinghurst, Australia; School of Biomedical Sciences, University of New South Wales, Australia
| | - Adelynn Tang
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia; School of Cancer Medicine, La Trobe University, Bundoora, Australia; Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Ajithkumar Vasanthakumar
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia; School of Cancer Medicine, La Trobe University, Bundoora, Australia; Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia.
| | - Kylie R James
- Garvan Institute of Medical Research, Darlinghurst, Australia; School of Biomedical Sciences, University of New South Wales, Australia.
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Doranga S, Krogfelt KA, Cohen PS, Conway T. Nutrition of Escherichia coli within the intestinal microbiome. EcoSal Plus 2024:eesp00062023. [PMID: 38417452 DOI: 10.1128/ecosalplus.esp-0006-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/03/2023] [Indexed: 03/01/2024]
Abstract
In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.
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Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Karen A Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark
| | - Paul S Cohen
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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10
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Robas M, Presa J, Arranz-Herrero J, Yildiz S, Rius-Rocabert S, Llinares-Pinel F, Probanza A, Schmolke M, Jiménez PA, Nistal-Villan E. Influenza A virus infection alters the resistance profile of gut microbiota to clinically relevant antibiotics. Microbiol Spectr 2024; 12:e0363522. [PMID: 38051056 PMCID: PMC10783141 DOI: 10.1128/spectrum.03635-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Influenza virus infection affects both lung and intestinal bacterial community composition. Most of the published analyses focus on the characterization of the microbiota composition changes. Here we assess functional alterations of gut microbiota such as nutrient and antibiotic resistance changes during an acute respiratory tract infection. Upon influenza A virus (IAV) infection, cecal microbiota drops accompanied by a decrease in the ability to metabolize some common nutrients under aerobic conditions. At the same time, the cecal community presents an increase in resistance against clinically relevant antibiotics, particularly cephalosporins. Functional characterization of complex communities presents an additional and necessary element of analysis that nowadays is mainly limited to taxonomic description. The consequences of these functional alterations could affect treatment strategies, especially in multimicrobial infections.
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Affiliation(s)
- Marina Robas
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
| | - Jesús Presa
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
| | - Javier Arranz-Herrero
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
- Facultad de Medicina, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo-CEU, Madrid, Spain
| | - Soner Yildiz
- Department of Microbiology and Molecular Medicine, Medical Faculty, University of Geneva, Geneva, Switzerland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sergio Rius-Rocabert
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
- Facultad de Medicina, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo-CEU, Madrid, Spain
- CEMBIO (Centre for Metabolomics and Bioanalysis), Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
| | - Francisco Llinares-Pinel
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
| | - Agustin Probanza
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
| | - Mirco Schmolke
- Department of Microbiology and Molecular Medicine, Medical Faculty, University of Geneva, Geneva, Switzerland
- Geneva Center of Inflammation Research, Medical Faculty, University of Geneva, Geneva, Switzerland
| | - Pedro A. Jiménez
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
| | - Estanislao Nistal-Villan
- Department of Pharmaceutical and Health Sciences School of Pharmacy, Microbiology Section, Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
- CEMBIO (Centre for Metabolomics and Bioanalysis), Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
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David C, Czauderna A, Cheng L, Lagune M, Jung HJ, Kim SG, Pamer EG, Prados J, Chen L, Becattini S. Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation. Gut Microbes 2024; 16:2340486. [PMID: 38659243 PMCID: PMC11057644 DOI: 10.1080/19490976.2024.2340486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) is a significant threat to public health worldwide. The primary reservoir for CR-Kp is the intestinal tract. There, the bacterium is usually present at low density but can bloom following antibiotic treatment, mostly in hospital settings. The impact of disturbances in the intestinal environment on the fitness, survival, expansion, and drug susceptibility of this pathogen is not well-understood, yet it may be relevant to devise strategies to tackle CR-Kp colonization and infection. Here, we adopted an in vivo model to examine the transcriptional adaptation of a CR-Kp clinical isolate to immune activation in the intestine. We report that as early as 6 hours following host treatment with anti-CD3 antibody, CR-Kp underwent rapid transcriptional changes including downregulation of genes involved in sugar utilization and amino acid biosynthesis and upregulation of genes involved in amino acid uptake and catabolism, antibiotic resistance, and stress response. In agreement with these findings, treatment increased the concentration of oxidative species and amino acids in the mouse intestine. Genes encoding for proteins containing the domain of unknown function (DUF) 1471 were strongly upregulated, however their deletion did not impair CR-Kp fitness in vivo upon immune activation. Transcription factor enrichment analysis identified the global regulator cAMP-Receptor Protein, CRP, as a potential orchestrator of the observed transcriptional signature. In keeping with the recognized role of CRP in regulating utilization of alternative carbon sources, crp deletion in CR-Kp resulted in strongly impaired gut colonization, although this effect was not amplified by immune activation. Thus, following intestinal colonization, which occurs in a CRP-dependent manner, CR-Kp can rapidly respond to immune cues by implementing a well-defined and complex transcriptional program whose direct relevance toward bacterial fitness warrants further investigation. Additional analyses utilizing this model may identify key factors to tackle CR-Kp colonization of the intestine.
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Affiliation(s)
- Clement David
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aleksander Czauderna
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Liqing Cheng
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marion Lagune
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Hea-Jin Jung
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Sohn G. Kim
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Eric G. Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Julien Prados
- Bioinformatics Support Platform for data analysis, Faculty of medicine, University of Geneva, Geneva, Switzerland
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Simone Becattini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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12
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Bleich RM, Li C, Sun S, Ahn JH, Dogan B, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Carroll IM, Simpson KW, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. MICROBIOME 2023; 11:277. [PMID: 38124090 PMCID: PMC10731797 DOI: 10.1186/s40168-023-01710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. RESULTS Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortium of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. CONCLUSIONS Our findings establish the in vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in vivo colonization dynamics of patient-derived bacteria in murine models. Video Abstract.
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Affiliation(s)
- Rachel M Bleich
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, Appalachian State University, Boone, NC, USA
| | - Chuang Li
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shan Sun
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ju-Hyun Ahn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Belgin Dogan
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Cassandra J Barlogio
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher A Broberg
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adrienne R Franks
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Bulik-Sullivan
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ian M Carroll
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth W Simpson
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Anthony A Fodor
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Janelle C Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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13
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Zangara MT, Darwish L, Coombes BK. Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. EcoSal Plus 2023; 11:eesp00182022. [PMID: 37220071 PMCID: PMC10729932 DOI: 10.1128/ecosalplus.esp-0018-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/04/2023] [Indexed: 01/28/2024]
Abstract
The microbiome of Crohn's disease (CD) patients is composed of a microbial community that is considered dysbiotic and proinflammatory in nature. The overrepresentation of Enterobacteriaceae species is a common feature of the CD microbiome, and much attention has been given to understanding the pathogenic role this feature plays in disease activity. Over 2 decades ago, a new Escherichia coli subtype called adherent-invasive E. coli (AIEC) was isolated and linked to ileal Crohn's disease. Since the isolation of the first AIEC strain, additional AIEC strains have been isolated from both inflammatory bowel disease (IBD) patients and non-IBD individuals using the original in vitro phenotypic characterization methods. Identification of a definitive molecular marker of the AIEC pathotype has been elusive; however, significant advancements have been made in understanding the genetic, metabolic, and virulence determinants of AIEC infection biology. Here, we review the current knowledge of AIEC pathogenesis to provide additional, objective measures that could be considered in defining AIEC and their pathogenic potential.
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Affiliation(s)
- Megan T. Zangara
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lena Darwish
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
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14
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Unni R, Andreani NA, Vallier M, Heinzmann SS, Taubenheim J, Guggeis MA, Tran F, Vogler O, Künzel S, Hövener JB, Rosenstiel P, Kaleta C, Dempfle A, Unterweger D, Baines JF. Evolution of E. coli in a mouse model of inflammatory bowel disease leads to a disease-specific bacterial genotype and trade-offs with clinical relevance. Gut Microbes 2023; 15:2286675. [PMID: 38059748 PMCID: PMC10730162 DOI: 10.1080/19490976.2023.2286675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a persistent inflammatory condition that affects the gastrointestinal tract and presents significant challenges in its management and treatment. Despite the knowledge that within-host bacterial evolution occurs in the intestine, the disease has rarely been studied from an evolutionary perspective. In this study, we aimed to investigate the evolution of resident bacteria during intestinal inflammation and whether- and how disease-related bacterial genetic changes may present trade-offs with potential therapeutic importance. Here, we perform an in vivo evolution experiment of E. coli in a gnotobiotic mouse model of IBD, followed by multiomic analyses to identify disease-specific genetic and phenotypic changes in bacteria that evolved in an inflamed versus a non-inflamed control environment. Our results demonstrate distinct evolutionary changes in E. coli specific to inflammation, including a single nucleotide variant that independently reached high frequency in all inflamed mice. Using ex vivo fitness assays, we find that these changes are associated with a higher fitness in an inflamed environment compared to isolates derived from non-inflamed mice. Further, using large-scale phenotypic assays, we show that bacterial adaptation to inflammation results in clinically relevant phenotypes, which intriguingly include collateral sensitivity to antibiotics. Bacterial evolution in an inflamed gut yields specific genetic and phenotypic signatures. These results may serve as a basis for developing novel evolution-informed treatment approaches for patients with intestinal inflammation.
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Affiliation(s)
- Rahul Unni
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Nadia Andrea Andreani
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Marie Vallier
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Silke S. Heinzmann
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Neuherberg, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Martina A. Guggeis
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Olga Vogler
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Künzel
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jan-Bernd Hövener
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Daniel Unterweger
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - John F. Baines
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
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15
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Kitamoto S, Kamada N. The oral-gut axis: a missing piece in the IBD puzzle. Inflamm Regen 2023; 43:54. [PMID: 37932859 PMCID: PMC10626704 DOI: 10.1186/s41232-023-00304-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial intractable intestinal disease. Focusing on only one facet of the pathogenesis of IBD is insufficient to fully capture the complexity of the disease, and results in limited advance in clinical management. Therefore, it is critical to dissect the interactions amongst the multifarious contributors to the pathogenesis to comprehensively understand its pathology and subsequently improve clinical outcomes. In this context, the systemic interactions between organs, particularly the oral-gut axis mediated by host immune cells and resident microorganisms, have garnered significant attention in IBD research. More specifically, periodontal disease such as periodontitis has been implicated in augmenting intestinal inflammation beyond the confines of the oral cavity. There is mounting evidence suggesting that potentially harmful oral resident bacteria, termed pathobionts, and pro-inflammatory immune cells from the oral mucosa can migrate to the gastrointestinal tract, thereby potentiating intestinal inflammation. This article aims to provide a holistic overview of the causal relationship between periodontal disease and intestinal inflammation. Furthermore, we will discuss potential determinants that facilitate the translocation of oral pathobionts into the gut, a key event underpinning the oral-gut axis. Unraveling the complex dynamics of microbiota and immunity in the oral-gut continuum will lead to a better understanding of the pathophysiology inherent in both oral and intestinal diseases and the development of prospective therapeutic strategies.
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Affiliation(s)
- Sho Kitamoto
- The World Premier International Research Center (WPI) Immunology Frontier Research Center (IFReC), 1012 IFReC Research Building, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Nobuhiko Kamada
- The World Premier International Research Center (WPI) Immunology Frontier Research Center (IFReC), 1012 IFReC Research Building, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
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16
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Faqerah N, Walker D, Gerasimidis K. Review article: The complex interplay between diet and Escherichia coli in inflammatory bowel disease. Aliment Pharmacol Ther 2023; 58:984-1004. [PMID: 37771255 DOI: 10.1111/apt.17720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/23/2022] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Although no causative microbe has been yet identified or successfully targeted in the treatment of inflammatory bowel disease (IBD), the role of Escherichia coli in the pathogenesis of Crohn's disease has attracted considerable interest. AIM In this review, we present a literature overview of the interactions between diet and E. coli and other Proteobacteria in the aetiology, outcomes and management of IBD and suggest future research directions. METHODS An extensive literature search was performed to identify in vitro studies and research in animal models that explored mechanisms by which dietary components can interact with E. coli or Proteobacteria to initiate or propagate gut inflammation. We also explored the effect diet and dietary therapies have on the levels of E. coli or Proteobacteria in patients with IBD. RESULTS Preclinical data suggest that the Western diet and its components influence the abundance, colonisation and phenotypic behaviour of E. coli in the gut, which may in turn initiate or contribute to gut inflammation. In contrast, the Mediterranean diet and specific dietary fibres may abrogate these effects and protect from inflammation. There are limited data from clinical trials, mostly from patients with Crohn's disease during treatment with exclusive enteral nutrition, with findings often challenging observations from preclinical research. Data from patients with ulcerative colitis are sparse. CONCLUSIONS Preclinical and some clinical trial data suggest that E. coli and other Proteobacteria interact with certain dietary components to promote gut inflammation. Well-designed clinical trials are required before dietary recommendations for disease management can be made.
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Affiliation(s)
- Nojoud Faqerah
- Human Nutrition, School of Medicine, Dentistry and Life Sciences, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, Glasgow, UK
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Microbiology, Rabigh Medical College, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Daniel Walker
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, Dentistry and Life Sciences, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, Glasgow, UK
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17
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Pascal Andreu V, Augustijn HE, Chen L, Zhernakova A, Fu J, Fischbach MA, Dodd D, Medema MH. gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Nat Biotechnol 2023; 41:1416-1423. [PMID: 36782070 PMCID: PMC10423304 DOI: 10.1038/s41587-023-01675-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2023] [Indexed: 02/15/2023]
Abstract
The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.
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Affiliation(s)
| | - Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lianmin Chen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Changzhou Medical Center, Nanjing Medical University, Changzhou, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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18
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Ye X, Liu B, Bai Y, Cao Y, Lin S, Lyu L, Meng H, Dai Y, Ye D, Pan W, Wang Z, Mao Y, Chen Q. Genetic evidence strengthens the bidirectional connection between gut microbiota and periodontitis: insights from a two-sample Mendelian randomization study. J Transl Med 2023; 21:674. [PMID: 37770955 PMCID: PMC10537583 DOI: 10.1186/s12967-023-04559-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/22/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Recent research has established the correlation between gut microbiota and periodontitis via oral-gut axis. Intestinal dysbiosis may play a pivotal bridging role in extra-oral inflammatory comorbidities caused by periodontitis. However, it is unclear whether the link is merely correlative or orchestrated by causative mechanistic interactions. This two-sample Mendelian randomization (MR) study was performed to evaluate the potential bidirectional causal relationships between gut microbiota and periodontitis. MATERIALS AND METHODS A two-sample MR analysis was performed using summary statistics from genome-wide association studies (GWAS) for gut microbiota (n = 18,340) and periodontitis (cases = 12,251; controls = 22,845). The inverse-variance weighted (IVW) method was used for the primary analysis, and we employed sensitivity analyses to assess the robustness of the main results. The PhenoScanner database was then searched for pleiotropy SNPs associated with potential confounders. In order to identify the possibly influential SNPs, we further conducted the leave-one-out analysis. Finally, a reverse MR analysis was performed to evaluate the possibility of links between periodontitis and genetically predicted gut microbiota alternation. RESULTS 2,699 single nucleotide polymorphisms (SNPs) associated with 196 microbiota genera were selected as instrumental variables (IVs). IVW method suggested that order Enterobacteriales (OR: 1.35, 95% CI 1.10-1.66), family Bacteroidales S24.7group (OR: 1.22, 95% CI 1.05-1.41), genus Lachnospiraceae UCG008 (OR: 1.16, 95% CI 1.03-1.31), genus Prevotella 7 (OR: 1.11, 95% CI 1.01-1.23), and order Pasteurellales (OR: 1.12, 95% CI 1.00-1.26) may be associated with a higher risk of periodontitis, while genus Ruminiclostridium 6 may be linked to a lower risk (OR: 0.82, 95% CI 0.70-0.95). The sensitivity and heterogeneity analyses yielded no indication of horizontal pleiotropy or heterogeneity. Only the association between order Enterobacteriales and the likelihood of periodontitis remained consistent across all alternative MR approaches. In the reverse MR analysis, four microbiota genera were genetically predicted to be down-regulated in periodontitis, whereas two were predicted to be up-regulated. CONCLUSIONS The present MR analysis demonstrated the potential bidirectional causal relationships between gut microbiota and periodontitis. Our research provided fresh insights for the prevention and management of periodontitis. Future research is required to support the finding of our current study.
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Affiliation(s)
- Xinjian Ye
- School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Stomatology Hospital, Cancer Center of Zhejiang University, Hangzhou, China
| | - Bin Liu
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yijing Bai
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yue Cao
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sirui Lin
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Linshuoshuo Lyu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, USA
| | - Haohao Meng
- School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Stomatology Hospital, Cancer Center of Zhejiang University, Hangzhou, China
| | - Yuwei Dai
- School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Stomatology Hospital, Cancer Center of Zhejiang University, Hangzhou, China
| | - Ding Ye
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Weiyi Pan
- School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Stomatology Hospital, Cancer Center of Zhejiang University, Hangzhou, China
| | - Zhiyong Wang
- School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Stomatology Hospital, Cancer Center of Zhejiang University, Hangzhou, China.
| | - Yingying Mao
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.
| | - Qianming Chen
- School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Stomatology Hospital, Cancer Center of Zhejiang University, Hangzhou, China.
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19
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Huang C, Pham HQ, Zhu L, Wang R, Law OK, Lin SL, Nie QC, Zhang L, Wang X, Lau TCK. Comparative Analysis of Transcriptome and Proteome Revealed the Common Metabolic Pathways Induced by Prevalent ESBL Plasmids in Escherichia coli. Int J Mol Sci 2023; 24:14009. [PMID: 37762311 PMCID: PMC10531281 DOI: 10.3390/ijms241814009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic resistance has emerged as one of the most significant threats to global public health. Plasmids, which are highly efficient self-replicating genetic vehicles, play a critical role in the dissemination of drug-resistant genes. Previous studies have mainly focused on drug-resistant genes only, often neglecting the complete functional role of multidrug-resistant (MDR) plasmids in bacteria. In this study, we conducted a comprehensive investigation of the transcriptomes and proteomes of Escherichia coli J53 transconjugants harboring six major MDR plasmids of different incompatibility (Inc) groups, which were clinically isolated from patients. The RNA-seq analysis revealed that MDR plasmids influenced the gene expression in the bacterial host, in particular, the genes related to metabolic pathways. A proteomic analysis demonstrated the plasmid-induced regulation of several metabolic pathways including anaerobic respiration and the utilization of various carbon sources such as serine, threonine, sialic acid, and galactarate. These findings suggested that MDR plasmids confer a growth advantage to bacterial hosts in the gut, leading to the expansion of plasmid-carrying bacteria over competitors without plasmids. Moreover, this study provided insights into the versatility of prevalent MDR plasmids in moderating the cellular gene network of bacteria, which could potentially be utilized in therapeutics development for bacteria carrying MDR plasmids.
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Affiliation(s)
- Chuan Huang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Hoa-Quynh Pham
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Lina Zhu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Rui Wang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Oi-Kwan Law
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Shu-Ling Lin
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Qi-Chang Nie
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Liang Zhang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Xin Wang
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China;
| | - Terrence Chi-Kong Lau
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
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20
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Bonet-Rossinyol Q, Camprubí-Font C, López-Siles M, Martinez-Medina M. Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells. Front Cell Infect Microbiol 2023; 13:1228159. [PMID: 37767199 PMCID: PMC10519790 DOI: 10.3389/fcimb.2023.1228159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/21/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction Adherent-invasive Escherichia coli (AIEC) is strongly associated with the pathogenesis of Crohn's disease (CD). However, no molecular markers currently exist for AIEC identification. This study aimed to identify differentially expressed genes (DEGs) between AIEC and non-AIEC strains that may contribute to AIEC pathogenicity and to evaluate their utility as molecular markers. Methods Comparative transcriptomics was performed on two closely related AIEC/non-AIEC strain pairs during Intestine-407 cell infection. DEGs were quantified by RT-qPCR in the same RNA extracts, as well as in 14 AIEC and 23 non-AIEC strains to validate the results across a diverse strain collection. Binary logistical regression was performed to identify DEGs whose quantification could be used as AIEC biomarkers. Results Comparative transcriptomics revealed 67 differences in expression between the two phenotypes in the strain pairs, 50 of which (81.97%) were corroborated by RT-qPCR. When explored in the whole strain collection, 29 DEGs were differentially expressed between AIEC and non-AIEC phenotypes (p-value < 0.042), and 42 genes between the supernatant fraction of infected cell cultures and the cellular fraction containing adhered and intracellular bacteria (p-value < 0.049). Notably, six DEGs detected in the strain collection were implicated in arginine biosynthesis and five in colanic acid synthesis. Furthermore, two biomarkers based on wzb and cueR gene expression were proposed with an accuracy of ≥ 85% in our strain collection. Discussion This is the first transcriptomic study conducted using AIEC-infected cell cultures. We have identified several genes that may be involved in AIEC pathogenicity, two of which are putative biomarkers for identification.
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21
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Cao Y, Zhang S, Tang L, Chen Y, Jiang S, Liu L, Gao X. Exploring the effects of Qijiao Shengbai capsule on leukopenic mice from the perspective of intestinbased on metabolomics and 16S rRNA sequencing. Heliyon 2023; 9:e19949. [PMID: 37810141 PMCID: PMC10559567 DOI: 10.1016/j.heliyon.2023.e19949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Qijiao Shengbai capsule (QJSB) is formulated according to the traditional Chinese medicine formula, its function is to nourish Qi and blood, improve the body's immunity. Leukopenia has been treated with it in clinical settings. However, the mechanism of leukopenia from the perspective of intestinal tract has not been reported. This study combined metabolomics and 16S rRNA sequencing technologies to investigate the mechanism of QJSB on leukopenia from the intestine. As a result of cyclophosphamide induction in mice, the results demonstrated that QJSB may greatly increase the quantity of peripheral leukocytes (including neutrophils). Meanwhile, QJSB had a restorative effect on the colon of leukopenic mice; it also increased the level of IL-2, IL-6 and G-CSF in the intestine, further enhancing the immunity and hematopoietic function of mice. Metabolic studies showed that QJSB altered 27 metabolites, most notably amino acid metabolism. In addition, QJSB had a positive regulatory effect on the intestinal microbiota, and could alter community composition by improving the diversity and abundance of the intestinal microbial, which mainly involved 6 related bacterial groups, and primarily regulates three associated SCFAs (acetic acid, butyrate acid and valeric acid). Therefore, this study suggests that QJSB can improve hematopoietic function, enhance the immune system, relieve leucopenia and improve the gut in leucopenic mice by modulating metabolic response pathways, fecal metabolites and intestinal microbiota.
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Affiliation(s)
- Yu Cao
- State Key Laboratory of Functions and Applications of Medicinal Plants and School of Pharmacy, Guizhou Medical University, Guiyang 550025, China
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Shuo Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants and School of Pharmacy, Guizhou Medical University, Guiyang 550025, China
- Experimental Animal Center of Guizhou Medical University, Guiyang 550025, China
| | - Li Tang
- State Key Laboratory of Functions and Applications of Medicinal Plants and School of Pharmacy, Guizhou Medical University, Guiyang 550025, China
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Yixuan Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants and School of Pharmacy, Guizhou Medical University, Guiyang 550025, China
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Siyue Jiang
- State Key Laboratory of Functions and Applications of Medicinal Plants and School of Pharmacy, Guizhou Medical University, Guiyang 550025, China
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Li Liu
- Guizhou Hanfang Pharmaceutical Co., Ltd., Guiyang 550002, China
| | - Xiuli Gao
- State Key Laboratory of Functions and Applications of Medicinal Plants and School of Pharmacy, Guizhou Medical University, Guiyang 550025, China
- Center of Microbiology and Biochemical Pharmaceutical Engineering, Guizhou Medical University, Guiyang 550025, China
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22
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Dang CV. Cancer Metabolism Historical Perspectives: A Chronicle of Controversies and Consensus. Cold Spring Harb Perspect Med 2023; 13:a041530. [PMID: 37553212 PMCID: PMC10691493 DOI: 10.1101/cshperspect.a041530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
A century ago, Otto Warburg's work sparked the field of cancer metabolism, which has since taken a tortuous path. As evidence accumulated over the decades, consensus views of causes of cancer emerged, whereby genetic and epigenetic oncogenic drivers promoted immune evasion and induced new blood vessels and neoplastic metabolism to support tumor growth. Neoplastic cells abandon social cues of intercellular cooperation, escape tissue confinement, metastasize, and ultimately kill the host. Herein, key milestones in the study of cancer metabolism are chronicled with an emphasis on carbohydrate metabolism. The field began with a cancer cell-autonomous view that has been refined by a richer understanding of solid cancers as growing, immune-suppressive, complex organs comprising different cell types that are nourished by a variety of nutrients and variable amounts of oxygen through abnormal neovasculatures. Based on foundational historical studies, our current understanding of cancer metabolism offers a hopeful outlook for targeting metabolism to enhance cancer therapy.
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Affiliation(s)
- Chi V Dang
- Ludwig Institute for Cancer Research, New York, New York 10017, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland 21287, USA
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23
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Zhao B, Osbelt L, Lesker TR, Wende M, Galvez EJC, Hönicke L, Bublitz A, Greweling-Pils MC, Grassl GA, Neumann-Schaal M, Strowig T. Helicobacter spp. are prevalent in wild mice and protect from lethal Citrobacter rodentium infection in the absence of adaptive immunity. Cell Rep 2023; 42:112549. [PMID: 37245209 DOI: 10.1016/j.celrep.2023.112549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/15/2023] [Accepted: 05/04/2023] [Indexed: 05/30/2023] Open
Abstract
Transfer of the gut microbiota from wild to laboratory mice alters the host's immune status and enhances resistance to infectious and metabolic diseases, but understanding of which microbes and how they promote host fitness is only emerging. Our analysis of metagenomic sequencing data reveals that Helicobacter spp. are enriched in wild compared with specific-pathogen-free (SPF) and conventionally housed mice, with multiple species commonly co-colonizing their hosts. We create laboratory mice harboring three non-SPF Helicobacter spp. to evaluate their effect on mucosal immunity and colonization resistance to the enteropathogen Citrobacter rodentium. Our experiments reveal that Helicobacter spp. interfere with C. rodentium colonization and attenuate C. rodentium-induced gut inflammation in wild-type (WT) mice, even preventing lethal infection in Rag2-/- SPF mice. Further analyses suggest that Helicobacter spp. interfere with tissue attachment of C. rodentium, putatively by reducing the availability of mucus-derived sugars. These results unveil pivotal protective functions of wild mouse microbiota constituents against intestinal infection.
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Affiliation(s)
- Bei Zhao
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging, and Modelling of Neuronal and Inflammatory Processes, Otto von Guericke University, Magdeburg, Germany
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging, and Modelling of Neuronal and Inflammatory Processes, Otto von Guericke University, Magdeburg, Germany
| | - Eric J C Galvez
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Lisa Hönicke
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Arne Bublitz
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Guntram A Grassl
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Center for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.
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24
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He L, Ding Y, Zhou X, Li T, Yin Y. Serine signaling governs metabolic homeostasis and health. Trends Endocrinol Metab 2023; 34:361-372. [PMID: 36967366 DOI: 10.1016/j.tem.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 05/12/2023]
Abstract
Serine has functions that are involved in metabolic homeostasis and health in pathological or stressful situations. Notably, the de novo serine synthesis pathway (SSP) plays a vital role in targeted regulation of immune responses, cell proliferation, and lipid/protein metabolism. The presentation of serine residues derived from SSP may be a signal of stress and provide novel insights into the relationship between metabolic homeostasis and diseases. Here, we summarize the current trends in understanding the regulatory mechanisms of serine metabolism, discuss how serine signaling governs metabolic and antistress processes, including oxidative stress, immunity, energy and lipid metabolism, intestinal microbiota, and the neurological system. We present a possible framework by which serine metabolism maintains metabolic homeostasis and treats human diseases.
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Affiliation(s)
- Liuqin He
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha 410081, China; CAS Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Processes, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha 410125, China.
| | - Yaqiong Ding
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha 410081, China; CAS Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Processes, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha 410125, China
| | - Xihong Zhou
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Processes, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha 410125, China
| | - Tiejun Li
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Processes, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha 410125, China.
| | - Yulong Yin
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Processes, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha 410125, China.
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25
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Bleich RM, Li C, Sun S, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Dogan B, Simpson KW, Carroll IM, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. RESEARCH SQUARE 2023:rs.3.rs-2899665. [PMID: 37214858 PMCID: PMC10197778 DOI: 10.21203/rs.3.rs-2899665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. Results Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. Conclusions Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.
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Affiliation(s)
| | - Chuang Li
- University of North Carolina at Chapel Hill
| | - Shan Sun
- University of North Carolina at Charlotte
| | | | | | | | | | - Belgin Dogan
- Cornell University College of Veterinary Medicine
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26
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Hua S, Lv B, Qiu Z, Li Z, Wang Z, Chen Y, Han Y, Tucker KL, Wu H, Jin W. Microbial metabolites in chronic heart failure and its common comorbidities. EMBO Mol Med 2023:e16928. [PMID: 37155563 DOI: 10.15252/emmm.202216928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
This study aimed to identify microbial signatures that contribute to the shared etiologies between chronic heart failure (CHF), type 2 diabetes, and chronic kidney disease. The serum levels of 151 microbial metabolites were measured in 260 individuals from the Risk Evaluation and Management of heart failure cohort, and it was found that those metabolites varied by an order of 105 fold. Out of 96 metabolites associated with the three cardiometabolic diseases, most were validated in two geographically independent cohorts. In all three cohorts, 16 metabolites including imidazole propionate (ImP) consistently showed significant differences. Notably, baseline ImP levels were three times higher in the Chinese compared with the Swedish cohorts and increased by 1.1-1.6 fold with each additional CHF comorbidity in the Chinese population. Cellular experiments further supported a causal link between ImP and distinct CHF relevant phenotypes. Additionally, key microbial metabolite-based risk scores were superior in CHF prognosis than the traditional Framingham or Get with the Guidelines-Heart Failure risk scores. Interactive visualization of these specific metabolite-disease links is available on our omics data server (https://omicsdata.org/Apps/REM-HF/).
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Affiliation(s)
- Sha Hua
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital and Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bomin Lv
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan Microbiome Center, Department of Bariatric and Metabolic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Zeping Qiu
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital and Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuojin Li
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital and Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyan Wang
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital and Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanjia Chen
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital and Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanxin Han
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital and Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Hao Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan Microbiome Center, Department of Bariatric and Metabolic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei Jin
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital and Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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27
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Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Willieme S, Kim K, Denike-Duval T, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Unravelling specific diet and gut microbial contributions to inflammatory bowel disease. RESEARCH SQUARE 2023:rs.3.rs-2518251. [PMID: 36993463 PMCID: PMC10055531 DOI: 10.21203/rs.3.rs-2518251/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic condition characterized by periods of spontaneous intestinal inflammation and is increasing in industrialized populations. Combined with host genetic predisposition, diet and gut bacteria are thought to be prominent features contributing to IBD, but little is known about the precise mechanisms involved. Here, we show that low dietary fiber promotes bacterial erosion of protective colonic mucus, leading to lethal colitis in mice lacking the IBD-associated cytokine, interleukin-10. Diet-induced inflammation is driven by mucin-degrading bacteria-mediated Th1 immune responses and is preceded by expansion of natural killer T cells and reduced immunoglobulin A coating of some bacteria. Surprisingly, an exclusive enteral nutrition diet, also lacking dietary fiber, reduced disease by increasing bacterial production of isobutyrate, which is dependent on the presence of a specific bacterial species, Eubacterium rectale. Our results illuminate a mechanistic framework using gnotobiotic mice to unravel the complex web of diet, host and microbial factors that influence IBD.
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Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica. T. Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mengrou Shan
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Li Zhang
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M. Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Costas A. Lyssiotis
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Grace Y. Chen
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kathryn A. Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mahesh S. Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, 5000 Odense, Denmark
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Casto-Rebollo C, Argente MJ, García ML, Blasco A, Ibáñez-Escriche N. Effect of environmental variance-based resilience selection on the gut metabolome of rabbits. Genet Sel Evol 2023; 55:15. [PMID: 36894894 PMCID: PMC9996918 DOI: 10.1186/s12711-023-00791-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Gut metabolites are key actors in host-microbiota crosstalk with effect on health. The study of the gut metabolome is an emerging topic in livestock, which can help understand its effect on key traits such as animal resilience and welfare. Animal resilience has now become a major trait of interest because of the high demand for more sustainable production. Composition of the gut microbiome can reveal mechanisms that underlie animal resilience because of its influence on host immunity. Environmental variance (VE), specifically the residual variance, is one measure of resilience. The aim of this study was to identify gut metabolites that underlie differences in the resilience potential of animals originating from a divergent selection for VE of litter size (LS). We performed an untargeted gut metabolome analysis in two divergent rabbit populations for low (n = 13) and high (n = 13) VE of LS. Partial least square-discriminant analysis was undertaken, and Bayesian statistics were computed to determine dissimilarities in the gut metabolites between these two rabbit populations. RESULTS We identified 15 metabolites that discriminate rabbits from the divergent populations with a prediction performance of 99.2% and 90.4% for the resilient and non-resilient populations, respectively. These metabolites were suggested to be biomarkers of animal resilience as they were the most reliable. Among these, five that derived from the microbiota metabolism (3-(4-hydroxyphenyl)lactate, 5-aminovalerate, and equol, N6-acetyllysine, and serine), were suggested to be indicators of dissimilarities in the microbiome composition between the rabbit populations. The abundances of acylcarnitines and metabolites derived from the phenylalanine, tyrosine, and tryptophan metabolism were low in the resilient population and these pathways can, therefore impact the inflammatory response and health status of animals. CONCLUSIONS This is the first study to identify gut metabolites that could act as potential resilience biomarkers. The results support differences in resilience between the two studied rabbit populations that were generated by selection for VE of LS. Furthermore, selection for VE of LS modified the gut metabolome, which could be another factor that modulates animal resilience. Further studies are needed to determine the causal role of these metabolites in health and disease.
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Affiliation(s)
- Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain
| | - María José Argente
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO_UMH), Miguel Hernández University, 03312, Orihuela, Spain
| | - María Luz García
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO_UMH), Miguel Hernández University, 03312, Orihuela, Spain
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain.
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29
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Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C. Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528811. [PMID: 36824941 PMCID: PMC9949166 DOI: 10.1101/2023.02.17.528811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, there is still a lack of approaches that allow to specifically modulate the abundance of individual microbes or microbial functions of interest. Moreover, current approaches for microbiome manipulation such as fecal transfers often entail a non-specific transfer of entire microbial communities with potentially unwanted side effects. To overcome this limitation, we here propose the concept of precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In a first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we present a metabolic modeling network framework that allows us to define precision prebiotics for a two-member C. elegans microbiome model community comprising the immune-protective Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. Thus, we predicted compounds that specifically boost the abundance of the host-beneficial MYb11, four of which were experimentally validated in vitro (L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid). L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that constraint-based metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Inga K Hamerich
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Reena Debray
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nancy Obeng
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Nutriinformatics, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
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30
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Arroyo-Mendoza M, Proctor A, Correa-Medina A, Brand MW, Rosas V, Wannemuehler MJ, Phillips GJ, Hinton DM. The E. coli pathobiont LF82 encodes a unique variant of σ 70 that results in specific gene expression changes and altered phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.523653. [PMID: 36798310 PMCID: PMC9934711 DOI: 10.1101/2023.02.08.523653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
LF82, an adherent invasive Escherichia coli pathobiont, is associated with ileal Crohn's disease, an inflammatory bowel disease of unknown etiology. Although LF82 contains no virulence genes, it carries several genetic differences, including single nucleotide polymorphisms (SNPs), that distinguish it from nonpathogenic E. coli. We have identified and investigated an extremely rare SNP that is within the highly conserved rpoD gene, encoding σ70, the primary sigma factor for RNA polymerase. We demonstrate that this single residue change (D445V) results in specific transcriptome and phenotypic changes that are consistent with multiple phenotypes observed in LF82, including increased antibiotic resistance and biofilm formation, modulation of motility, and increased capacity for methionine biosynthesis. Our work demonstrates that a single residue change within the bacterial primary sigma factor can lead to multiple alterations in gene expression and phenotypic changes, suggesting an underrecognized mechanism by which pathobionts and other strain variants with new phenotypes can emerge.
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Affiliation(s)
- Melissa Arroyo-Mendoza
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Alexandra Proctor
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Abraham Correa-Medina
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
| | - Meghan Wymore Brand
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Virginia Rosas
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
| | - Michael J Wannemuehler
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Gregory J Phillips
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
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Abstract
The surge in inflammatory bowel diseases, like Crohn's disease (CD), is alarming. While the role of the gut microbiome in CD development is unresolved, the frequent isolation of adherent-invasive Escherichia coli (AIEC) strains from patient biopsies, together with their propensity to trigger gut inflammation, underpin the potential role of these bacteria as disease modifiers. In this review, we explore the spectrum of AIEC pathogenesis, including their metabolic versatility in the gut. We describe how AIEC strains hijack the host defense mechanisms to evade immune attrition and promote inflammation. Furthermore, we highlight the key traits that differentiate AIEC from commensal E. coli. Deciphering the main components of AIEC virulence is cardinal to the discovery of the next generation of antimicrobials that can selectively eradicate CD-associated bacteria.
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Affiliation(s)
- Sarah Mansour
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada
| | - Tahreem Asrar
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada
| | - Wael Elhenawy
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada,Division of Gastroenterology, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada,Li Ka Shing Institute of Virology, Canada,Women and Children’s Health Research Institute, Edmonton, Alberta, Canada,Antimicrobial Resistance, One Health Consortium - Edmonton, AB, Canada,CONTACT Wael Elhenawy Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta
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32
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Tanaka R, Imai J, Tsugawa H, Eap KB, Yazawa M, Kaneko M, Ohno M, Sugihara K, Kitamoto S, Nagao-Kitamoto H, Barnich N, Matsushima M, Suzuki T, Kagawa T, Nishizaki Y, Suzuki H, Kamada N, Hozumi K. Adherent-invasive E. coli - induced specific IgA limits pathobiont localization to the epithelial niche in the gut. Front Microbiol 2023; 14:1031997. [PMID: 36910191 PMCID: PMC9995611 DOI: 10.3389/fmicb.2023.1031997] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Background and aim Adherent-invasive E. coli (AIEC) has been identified as a pathobiont associated with Crohn's disease (CD), that prefers to grow in inflammatory conditions. Although the colonization by AIEC is implicated in the progression of the disease and exacerbates inflammation in murine colitis models, the recognition and response of host immunity to AIEC remains elusive. Methods Antibiotic treated female C57BL/6 mice were inoculated by commensal E. coli and LF82 AIEC strains. Luminal-IgA fractions were prepared from feces and their binding to AIEC and other strains was assessed to confirm specificity. IgA binding to isogenic mutant strains was performed to identify the functional molecules that are recognized by AIEC specific IgA. The effect of IgA on epithelial invasion of LF82 strain was confirmed using in vitro invasion assay and in vivo colonization of the colonic epithelium. Results Persistent colonization by AIEC LF82 induced secretion of luminal IgA, while commensal E. coli strain did not. Induced anti-LF82 IgA showed specific binding to other AIEC strains but not to the commensal, non-AIEC E. coli strains. Induced IgA showed decreased binding to LF82 strains with mutated adhesin and outer membrane proteins which are involved in AIEC - epithelial cell interaction. Consistently, LF82-specific IgA limited the adhesion and invasion of LF82 in cultured epithelial cells, which seems to be required for the elimination in the colonic epithelium in mice. Conclusion These results demonstrate that host immunity selectively recognizes pathobiont E. coli, such as AIEC, and develop specific IgA. The induced IgA specific to pathobiont E. coli, in turn, contributes to preventing the pathobionts from accessing the epithelium.
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Affiliation(s)
- Rika Tanaka
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
| | - Jin Imai
- Division of Gastroenterology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan.,Department of Clinical Health Science, Tokai University School of Medicine, Isehara, Japan
| | - Hitoshi Tsugawa
- Transkingdom Signaling Research Unit, Division of Host Defense, Tokai University School of Medicine, Isehara, Japan
| | - Karl Bil Eap
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
| | - Masaki Yazawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
| | - Motoki Kaneko
- Division of Gastroenterology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Masashi Ohno
- Division of Gastroenterology, Shiga University of Medical Science, Otsu, Japan
| | - Kohei Sugihara
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Sho Kitamoto
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.,WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Hiroko Nagao-Kitamoto
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.,WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Nicolas Barnich
- UMR1071 Inserm/University Clermont Auvergne, INRAE USC2018, M2iSH, CRNH Auvergne, Clermont-Ferrand, France
| | - Masashi Matsushima
- Division of Gastroenterology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Takayoshi Suzuki
- Division of Gastroenterology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Tatehiro Kagawa
- Division of Gastroenterology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Yasuhiro Nishizaki
- Department of Clinical Health Science, Tokai University School of Medicine, Isehara, Japan
| | - Hidekazu Suzuki
- Division of Gastroenterology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.,WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Katsuto Hozumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
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Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus. Nat Commun 2022; 13:7718. [PMID: 36513659 PMCID: PMC9748033 DOI: 10.1038/s41467-022-35380-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients' exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.
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34
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Dietary regulation in health and disease. Signal Transduct Target Ther 2022; 7:252. [PMID: 35871218 PMCID: PMC9308782 DOI: 10.1038/s41392-022-01104-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/21/2022] [Accepted: 07/04/2022] [Indexed: 02/08/2023] Open
Abstract
Nutriments have been deemed to impact all physiopathologic processes. Recent evidences in molecular medicine and clinical trials have demonstrated that adequate nutrition treatments are the golden criterion for extending healthspan and delaying ageing in various species such as yeast, drosophila, rodent, primate and human. It emerges to develop the precision-nutrition therapeutics to slow age-related biological processes and treat diverse diseases. However, the nutritive advantages frequently diversify among individuals as well as organs and tissues, which brings challenges in this field. In this review, we summarize the different forms of dietary interventions extensively prescribed for healthspan improvement and disease treatment in pre-clinical or clinical. We discuss the nutrient-mediated mechanisms including metabolic regulators, nutritive metabolism pathways, epigenetic mechanisms and circadian clocks. Comparably, we describe diet-responsive effectors by which dietary interventions influence the endocrinic, immunological, microbial and neural states responsible for improving health and preventing multiple diseases in humans. Furthermore, we expatiate diverse patterns of dietotheroapies, including different fasting, calorie-restricted diet, ketogenic diet, high-fibre diet, plants-based diet, protein restriction diet or diet with specific reduction in amino acids or microelements, potentially affecting the health and morbid states. Altogether, we emphasize the profound nutritional therapy, and highlight the crosstalk among explored mechanisms and critical factors to develop individualized therapeutic approaches and predictors.
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35
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Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
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Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
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36
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Zhao C, Bao L, Qiu M, Wu K, Zhao Y, Feng L, Xiang K, Zhang N, Hu X, Fu Y. Commensal cow Roseburia reduces gut-dysbiosis-induced mastitis through inhibiting bacterial translocation by producing butyrate in mice. Cell Rep 2022; 41:111681. [DOI: 10.1016/j.celrep.2022.111681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/17/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022] Open
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Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae. Nat Commun 2022; 13:5617. [PMID: 36153315 PMCID: PMC9509339 DOI: 10.1038/s41467-022-33313-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
Infections by multidrug-resistant Enterobacteriaceae (MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization. Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients. Multidrug-resistant Enterobacteriaceae (MRE) represent a major threat for patients’ health. Here, the authors describe how cooperation between gut commensal bacteria (Lactobacillus spp. And Clostridiales) restrict MRE colonization in mice and patients
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38
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Yu QQ, Zhang H, Zhao S, Xie D, Zhao H, Chen W, Pang M, Han B, Jiang P. Systematic evaluation of irinotecan-induced intestinal mucositis based on metabolomics analysis. Front Pharmacol 2022; 13:958882. [PMID: 36188576 PMCID: PMC9520243 DOI: 10.3389/fphar.2022.958882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chemotherapy-induced intestinal mucositis (CIM) is a major dose-limiting side effect of chemotherapy, especially in regimens containing irinotecan (CPT-11). Several studies on the pathologic mechanisms of CIM focused on both the genomics and molecular pathways triggered by chemotherapy. However, systematic evaluation of metabolomic analysis in irinotecan-induced intestinal mucositis (IIM) has not been investigated. This study aimed to comprehensively analyze metabolite changes in main tissues of IIM mouse models. Male ICR mice were assigned to two groups: the model group (n = 11) treated with CPT-11 (20 mg/kg daily; i.p.) and the control group (n= 11) with solvent for 9 days. Gas chromatography-mass spectrometry (GC-MS) was used to investigate the metabolic alterations in the serum, intestinal, colonic, hepatic, and splenic samples of mice between two groups by multivariate statistical analyses, including GC–MS data processing, pattern recognition analysis, and pathway analysis. Forty-six metabolites, including hydrocarbons, amino acids, lipids, benzenoids, hydroxy acids, and amines, had significant changes in levels in tissues and sera of IIM mouse models. The most important pathways related to the identified metabolites were the glycerolipid metabolism in the colon and aminoacyl-tRNA biosynthesis; glycine, serine, and threonine metabolism; and glyoxylate and dicarboxylate metabolism in the liver. Our study firstly provided a comprehensive and systematic view of metabolic alterations of IIM using GC-MS analysis. The characterizations of metabolic changes could offer profound and theoretical insight into exploring new biomarkers for diagnosis and treatment of IIM.
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Affiliation(s)
- Qing-Qing Yu
- Laboratory of Biochemistry and Biomedical Materials, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Heng Zhang
- Department of Laboratory, Shandong Daizhuang Hospital, Jining, China
| | - Shiyuan Zhao
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Dadi Xie
- Department of Endocrine, Tengzhou Central People’s Hospital, Tengzhou, China
| | - Haibo Zhao
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Weidong Chen
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Min Pang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Baoqin Han
- Laboratory of Biochemistry and Biomedical Materials, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Baoqin Han, ; Pei Jiang,
| | - Pei Jiang
- Jining First People’s Hospital, Jining Medical College, Jining, China
- *Correspondence: Baoqin Han, ; Pei Jiang,
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Brauer AL, Learman BS, Taddei SM, Deka N, Hunt BC, Armbruster CE. Preferential catabolism of l- vs d-serine by Proteus mirabilis contributes to pathogenesis and catheter-associated urinary tract infection. Mol Microbiol 2022; 118:125-144. [PMID: 35970717 PMCID: PMC9486832 DOI: 10.1111/mmi.14968] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/24/2022] [Accepted: 07/30/2022] [Indexed: 11/29/2022]
Abstract
Proteus mirabilis is a common cause of urinary tract infection, especially in catheterized individuals. Amino acids are the predominant nutrient for bacteria during growth in urine, and our prior studies identified several amino acid import and catabolism genes as fitness factors for P. mirabilis catheter-associated urinary tract infection (CAUTI), particularly those for d- and l-serine. In this study, we sought to determine the hierarchy of amino acid utilization by P. mirabilis and to examine the relative importance of d- vs l-serine catabolism for critical steps in CAUTI development and progression. Herein, we show that P. mirabilis preferentially catabolizes l-serine during growth in human urine, followed by d-serine, threonine, tyrosine, glutamine, tryptophan, and phenylalanine. Independently disrupting catabolism of either d- or l-serine has minimal impact on in vitro phenotypes while completely disrupting both pathways decreases motility, biofilm formation, and fitness due to perturbation of membrane potential and cell wall biosynthesis. In a mouse model of CAUTI, loss of either serine catabolism system decreased fitness, but disrupting l-serine catabolism caused a greater fitness defect than disrupting d-serine catabolism. We, therefore, conclude that the hierarchical utilization of amino acids may be a critical component of P. mirabilis colonization and pathogenesis within the urinary tract.
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Affiliation(s)
- Aimee L. Brauer
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Brian S. Learman
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Steven M. Taddei
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Namrata Deka
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Benjamin C. Hunt
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Chelsie E. Armbruster
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
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Zhang P. Influence of Foods and Nutrition on the Gut Microbiome and Implications for Intestinal Health. Int J Mol Sci 2022; 23:ijms23179588. [PMID: 36076980 PMCID: PMC9455721 DOI: 10.3390/ijms23179588] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Food components in our diet provide not only necessary nutrients to our body but also substrates for the mutualistic microbial flora in our gastrointestinal tract, termed the gut microbiome. Undigested food components are metabolized to a diverse array of metabolites. Thus, what we eat shapes the structure, composition, and function of the gut microbiome, which interacts with the gut epithelium and mucosal immune system and maintains intestinal homeostasis in a healthy state. Alterations of the gut microbiome are implicated in many diseases, such as inflammatory bowel disease (IBD). There is growing interest in nutritional therapy to target the gut microbiome in IBD. Investigations into dietary effects on the composition changes in the gut microbiome flourished in recent years, but few focused on gut physiology. This review summarizes the current knowledge regarding the impacts of major food components and their metabolites on the gut and health consequences, specifically within the GI tract. Additionally, the influence of the diet on the gut microbiome-host immune system interaction in IBD is also discussed. Understanding the influence of the diet on the interaction of the gut microbiome and the host immune system will be useful in developing nutritional strategies to maintain gut health and restore a healthy microbiome in IBD.
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Affiliation(s)
- Ping Zhang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
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Mei H, Yang S, Peng A, Li R, Xiang F, Zheng H, Tan Y, Zhang Y, Zhou A, Zhang J, Xiao H. Development of the gut microbiota in healthy twins during the first 2 years of life and associations with body mass index z-score: Results from the Wuhan twin birth cohort study. Front Microbiol 2022; 13:891679. [PMID: 36060734 PMCID: PMC9433903 DOI: 10.3389/fmicb.2022.891679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota undergoes rapid and vital changes to microbial community structure and the microbial-immune crosstalk during the first 3 years of life, which is thought to be involved in the pathobiology of later-life disease. Compared to single-born children, little is known about the gut microbiota of twins in early childhood. Based on the Wuhan Twin Birth Cohort study, 344 stool samples from 204 twin families were analyzed to investigate the difference in gut microbiota composition at 6, 12, and 24 months of age. Furthermore, this study evaluated the association between gut microbiota development curves and body mass index z-score (BMI_Z) curves at 6, 12, and 24 months of age. The predominant microbiota phyla identified in twins were Proteobacteria, Actinobacteriota, Firmicutes, Bacteroidota, and Verrucomicrobiota. The richness and diversity of gut microbiota increased from 6 to 24 months old (alpha diversity with p < 0.05). Beta diversity revealed 61 gut microbiota genera that were significantly different in relative abundance among the three age groups. Among the 61 gut microbiota genera, 30 distinct trajectory curves (DTCs) were generated by group-based trajectory models after log2 transformation of their relative abundance. Subsequently, Spearman correlation analysis revealed that only five gut microbiota DTC were correlated with the BMI_Z DTC. Therefore, we further examined the association between the five gut microbiota genera DTC and BMI_Z DTC using generalized estimation equation models. The results revealed a significant association between the DTC groups of Parabacteroides and that of BMI_Z (coefficient = 0.75, p = 0.04). The results of this study validated the hypothesis that the richness and diversity of gut microbiota developed with age in twins. Moreover, participants with a higher DTC of log2-transformed Parabacteroides had a higher BMI_Z DTC during the first 2 years of life. Further studies are needed to confirm the association between Parabacteroides and BMI_Z in other populations.
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Affiliation(s)
- Hong Mei
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Maternal and Child Health Care, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaoping Yang
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - An’na Peng
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruizhen Li
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feiyan Xiang
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Zheng
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yafei Tan
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ya Zhang
- Department of Maternal and Child Health Care, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ai’fen Zhou
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianduan Zhang
- Department of Maternal and Child Health Care, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Han Xiao
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Rzeznitzeck J, Breves G, Rychlik I, Hoerr FJ, von Altrock A, Rath A, Rautenschlein S. The effect of Campylobacter jejuni and Campylobacter coli colonization on the gut morphology, functional integrity, and microbiota composition of female turkeys. Gut Pathog 2022; 14:33. [PMID: 35922874 PMCID: PMC9347085 DOI: 10.1186/s13099-022-00508-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Campylobacter (C.) species are the most common bacterial cause of foodborne diarrhea in humans. Despite colonization, most animals do not show clinical signs, making recognition of affected flocks and disruption of the infection chain before slaughter challenging. Turkeys are often cocolonized with C. jejuni and C. coli. To understand the pathogen-host-interaction in the context of two different Campylobacter species, we compared the colonization patterns and quantities in mono- and co-colonized female commercial turkeys. In three repeated experiments we investigated the impact on gut morphology, functional integrity, and microbiota composition as parameters of gut health at seven, 14, and 28 days post-inoculation. RESULTS Despite successful Campylobacter colonization, clinical signs or pathological lesions were not observed. C. coli persistently colonized the distal intestinal tract and at a higher load compared to C. jejuni. Both strains were isolated from livers and spleens, occurring more frequently in C. jejuni- and co-inoculated turkeys. Especially in C. jejuni-positive animals, translocation was accompanied by local heterophil infiltration, villus blunting, and shallower crypts. Increased permeability and lower electrogenic ion transport of the cecal mucosa were also observed. A lower relative abundance of Clostridia UCG-014, Lachnospiraceae, and Lactobacillaceae was noted in all inoculated groups compared to controls. CONCLUSIONS In sum, C. jejuni affects gut health and may interfere with productivity in turkeys. Despite a higher cecal load, the impact of C. coli on investigated parameters was less pronounced. Interestingly, gut morphology and functional integrity were also less affected in co-inoculated animals while the C. jejuni load decreased over time, suggesting C. coli may outcompete C. jejuni. Since a microbiota shift was observed in all inoculated groups, future Campylobacter intervention strategies may involve stabilization of the gut microbiota, making it more resilient to Campylobacter colonization in the first place.
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Affiliation(s)
- Janina Rzeznitzeck
- Clinic for Poultry, University of Veterinary Medicine Hannover, Foundation, Buenteweg 17, 30559, Hannover, Germany
| | - Gerhard Breves
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Frederic J Hoerr
- Veterinary Diagnostics Pathology, LLC, 638 South Fort Valley Road, VA, 22652, Fort Valley, United States of America
| | - Alexandra von Altrock
- Clinic for Swine, Small Ruminants and Forensic Medicine, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Alexandra Rath
- Clinic for Swine, Small Ruminants and Forensic Medicine, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Foundation, Buenteweg 17, 30559, Hannover, Germany.
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Cernava T, Berg G. The emergence of disease-preventing bacteria within the plant microbiota. Environ Microbiol 2022. [PMID: 35001485 DOI: 10.1111/1462-2920-15896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Microbiome studies have facilitated the discovery of harmful as well as beneficial microorganisms over the last years. Recently, distinct bacteria were found within the microbiota of crop plants that confer disease resistance to their hosts. Although it is well known that the interplay between microbes and plants can result in improved plant health, the phenomenon of holistically disease-preventing bacteria is new. Here, we put the recent discoveries of disease-preventing bacteria in context with decade-long plant microbiome research that has preceded them. In addition, we provide explanations as to why disease resistance in certain plants, mediated by specific bacteria, has only recently been discovered. We argue that such findings were primarily limited by technological constraints and that analogous findings are very likely to be made with other plant species. The general concept may even be extendable to additional groups of organisms. We, therefore, suggest the introduction of the specific term soterobiont in order to facilitate an unambiguous definition of disease-preventing microorganisms within the microbiota of higher organisms.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz-Institute for Agricultural Engineering Potsdam, Potsdam, 14469, Germany
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Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N. Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Cell Rep 2022; 40:111093. [PMID: 35858565 PMCID: PMC10903618 DOI: 10.1016/j.celrep.2022.111093] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/26/2022] [Accepted: 06/21/2022] [Indexed: 12/26/2022] Open
Abstract
Pathobionts employ unique metabolic adaptation mechanisms to maximize their growth in disease conditions. Adherent-invasive Escherichia coli (AIEC), a pathobiont enriched in the gut mucosa of patients with inflammatory bowel disease (IBD), utilizes diet-derived L-serine to adapt to the inflamed gut. Therefore, the restriction of dietary L-serine starves AIEC and limits its fitness advantage. Here, we find that AIEC can overcome this nutrient limitation by switching the nutrient source from the diet to the host cells in the presence of mucolytic bacteria. During diet-derived L-serine restriction, the mucolytic symbiont Akkermansia muciniphila promotes the encroachment of AIEC to the epithelial niche by degrading the mucus layer. In the epithelial niche, AIEC acquires L-serine from the colonic epithelium and thus proliferates. Our work suggests that the indirect metabolic network between pathobionts and commensal symbionts enables pathobionts to overcome nutritional restriction and thrive in the gut.
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Affiliation(s)
- Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Prakaimuk Saraithong
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Hiroko Nagao-Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Matthew Hoostal
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Caroline McCarthy
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Rosevelt
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Merritt G Gillilland
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jin Imai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maiko Omi
- Department of Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Shrinivas Bishu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Nicolas Barnich
- M2iSH, UMR1071 Inserm/University Clermont Auvergne, Clermont-Ferrand, France
| | - Thomas M Schmidt
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Asma Nusrat
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan L Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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Kitamoto S, Kamada N. Periodontal connection with intestinal inflammation: Microbiological and immunological mechanisms. Periodontol 2000 2022; 89:142-153. [PMID: 35244953 PMCID: PMC9018512 DOI: 10.1111/prd.12424] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Humans have coevolved with the trillions of resident microbes that populate every nook and cranny of the body. At each site, the resident microbiota creates a unique ecosystem specialized to its environment, benefiting the development and maintenance of human physiology through harmonious symbiotic relationships with the host. However, when the resident microbiota is perturbed, significant complications may arise with disastrous consequences that affect the local and distant ecosystems. In this context, periodontal disease results in inflammation beyond the oral cavity, such as in the gastrointestinal tract. Accumulating evidence indicates that potentially harmful oral resident bacteria (referred to as pathobionts) and pathogenic immune cells in the oral mucosa can migrate to the lower gastrointestinal tract and contribute to intestinal inflammation. We will review the most recent advances concerning the periodontal connection with intestinal inflammation from microbiological and immunological perspectives. Potential therapeutic approaches that target the connection between the mouth and the gut to treat gastrointestinal diseases, such as inflammatory bowel disease, will be examined. Deciphering the complex interplay between microbes and immunity along the mouth-gut axis will provide a better understanding of the pathogenesis of both oral and gut pathologies and present therapeutic opportunities.
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Affiliation(s)
- Sho Kitamoto
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineUniversity of MichiganAnn ArborMichiganUSA
| | - Nobuhiko Kamada
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineUniversity of MichiganAnn ArborMichiganUSA
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Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes. Mucosal Immunol 2022; 15:1071-1084. [PMID: 35970917 DOI: 10.1038/s41385-022-00553-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023]
Abstract
Advances in technology and software have radically expanded the scope of metabolomics studies and allow us to monitor a broad transect of central carbon metabolism in routine studies. These increasingly sophisticated tools have shown that many human diseases are modulated by microbial metabolism. Despite this, it remains surprisingly difficult to move beyond these statistical associations and identify the specific molecular mechanisms that link dysbiosis to the progression of human disease. This difficulty stems from both the biological intricacies of host-microbiome dynamics as well as the analytical complexities inherent to microbiome metabolism research. The primary objective of this review is to examine the experimental and computational tools that can provide insights into the molecular mechanisms at work in host-microbiome interactions and to highlight the undeveloped frontiers that are currently holding back microbiome research from fully leveraging the benefits of modern metabolomics.
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Liu Y, Liu C, Wu H, Meng Q, Zhou Z. Small Intestine Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers. Front Microbiol 2022; 13:862151. [PMID: 35531283 PMCID: PMC9069012 DOI: 10.3389/fmicb.2022.862151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
The gastrointestinal tract (GIT) contains complex microbial communities and plays an essential role in the overall health of the host. Previous studies of beef cattle feed efficiency have primarily concentrated on the ruminal microbiota because it plays a key role in energy production and nutrient supply in the host. Although the small intestine is the important site of post-ruminal digestion and absorption of nutrients, only a few studies have explored the relationship between the microbial populations in the small intestine and feed efficiency. Moreover, variations in GIT metabolites contribute to differences in feed efficiency. The objective of this study was to investigate relationships among bacterial populations of duodenum, jejunum, ileum; microbial metabolites; and RFI phenotype of beef cattle. We carried out by using Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC–MS). In the duodenum, the relative abundances of Firmicutes ( p < 0.01), Lachnospiraceae, Ruminococcaceae, Family_XIII, Christensenellaceae, Christensenellaceae_R-7_group ( p < 0.05), and Lachnospiraceae_NK3A20_group ( p < 0.05) were higher in the low residual feed intake (LRFI) group compared with the high residual feed intake (HRFI) group, whereas the HRFI group had higher abundances of Proteobacteria and Acinetobacter ( p < 0.01). In the jejunum, the relative abundances of Lachnospiraceae and Lachnospiraceae_NK3A20_group were higher in the LRFI group ( p < 0.05). In the ileum, the relative abundances of Ruminococcaceae ( p < 0.01), Christensenellaceae, Christensenellaceae_R-7_group, and Ruminococcus_2 were also higher in the LRFI group ( p < 0.05). Moreover, the genera Lachnospiraceae_NK3A20_group, Christensenellaceae_R-7_group, and Ruminococcus_2 were negatively associated with RFI, while the genus Acinetobacter was positively associated with RFI. The metabolomics analysis revealed that the LRFI group significantly improved protein digestion and absorption, as well as glycerophospholipid metabolism in the duodenum, jejunum, ileum. The correlation between intestinal microorganisms and metabolites revealed that some microorganisms play an important role in amino acid metabolism, glycerophospholipid metabolism, nutrient digestion and absorption, and antioxidant enhancement. The present study provides a better understanding of the small intestinal microbiota and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chang Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Mashaqi S, Kallamadi R, Matta A, Quan SF, Patel SI, Combs D, Estep L, Lee-Iannotti J, Smith C, Parthasarathy S, Gozal D. Obstructive Sleep Apnea as a Risk Factor for COVID-19 Severity-The Gut Microbiome as a Common Player Mediating Systemic Inflammation via Gut Barrier Dysfunction. Cells 2022; 11:1569. [PMID: 35563874 PMCID: PMC9101605 DOI: 10.3390/cells11091569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
The novel corona virus that is now known as (SARS-CoV-2) has killed more than six million people worldwide. The disease presentation varies from mild respiratory symptoms to acute respiratory distress syndrome and ultimately death. Several risk factors have been shown to worsen the severity of COVID-19 outcomes (such as age, hypertension, diabetes mellitus, and obesity). Since many of these risk factors are known to be influenced by obstructive sleep apnea, this raises the possibility that OSA might be an independent risk factor for COVID-19 severity. A shift in the gut microbiota has been proposed to contribute to outcomes in both COVID-19 and OSA. To further evaluate the potential triangular interrelationships between these three elements, we conducted a thorough literature review attempting to elucidate these interactions. From this review, it is concluded that OSA may be a risk factor for worse COVID-19 clinical outcomes, and the shifts in gut microbiota associated with both COVID-19 and OSA may mediate processes leading to bacterial translocation via a defective gut barrier which can then foster systemic inflammation. Thus, targeting biomarkers of intestinal tight junction dysfunction in conjunction with restoring gut dysbiosis may provide novel avenues for both risk detection and adjuvant therapy.
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Affiliation(s)
- Saif Mashaqi
- Department of Pulmonary, Allergy, Critical Care and Sleep Medicine, The University of Arizona College of Medicine, Tucson, AZ 85719, USA; (S.F.Q.); (S.I.P.); (D.C.); (L.E.); (S.P.)
| | - Rekha Kallamadi
- Department of Internal Medicine, The University of North Dakota School of Medicine, Grand Forks, ND 58203, USA; (R.K.); (A.M.)
| | - Abhishek Matta
- Department of Internal Medicine, The University of North Dakota School of Medicine, Grand Forks, ND 58203, USA; (R.K.); (A.M.)
| | - Stuart F. Quan
- Department of Pulmonary, Allergy, Critical Care and Sleep Medicine, The University of Arizona College of Medicine, Tucson, AZ 85719, USA; (S.F.Q.); (S.I.P.); (D.C.); (L.E.); (S.P.)
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Salma I. Patel
- Department of Pulmonary, Allergy, Critical Care and Sleep Medicine, The University of Arizona College of Medicine, Tucson, AZ 85719, USA; (S.F.Q.); (S.I.P.); (D.C.); (L.E.); (S.P.)
| | - Daniel Combs
- Department of Pulmonary, Allergy, Critical Care and Sleep Medicine, The University of Arizona College of Medicine, Tucson, AZ 85719, USA; (S.F.Q.); (S.I.P.); (D.C.); (L.E.); (S.P.)
| | - Lauren Estep
- Department of Pulmonary, Allergy, Critical Care and Sleep Medicine, The University of Arizona College of Medicine, Tucson, AZ 85719, USA; (S.F.Q.); (S.I.P.); (D.C.); (L.E.); (S.P.)
| | - Joyce Lee-Iannotti
- Department of Sleep Medicine, The University of Arizona College of Medicine, Phoenix, AZ 85006, USA;
| | - Charles Smith
- The Intermountain Healthcare, Merrill Gappmayer Family Medicine Center, Provo, UT 84604, USA;
| | - Sairam Parthasarathy
- Department of Pulmonary, Allergy, Critical Care and Sleep Medicine, The University of Arizona College of Medicine, Tucson, AZ 85719, USA; (S.F.Q.); (S.I.P.); (D.C.); (L.E.); (S.P.)
| | - David Gozal
- Department of Child Health, University of Missouri School of Medicine, Columbia, MO 65201, USA;
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Zhang S, Morgan XC, Dogan B, Martin FP, Strickler SR, Oka A, Herzog J, Liu B, Dowd SE, Huttenhower C, Pichaud M, Dogan EI, Satsangi J, Longman R, Yantiss R, Mueller LA, Scherl E, Sartor RB, Simpson KW. Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn's disease. JCI Insight 2022; 7:157013. [PMID: 35413017 PMCID: PMC9220930 DOI: 10.1172/jci.insight.157013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance to diarrheal and inflammatory bowel diseases across species. Here, we integrated the microbial and chemical microenvironment of a patient’s ileal mucosa with their clinical phenotype and genotype to identify factors favoring the growth and virulence of adherent and invasive E. coli (AIEC) linked to Crohn’s disease. We determined that the ileal niche of AIEC was characterized by inflammation, dysbiosis, coculture of Enterococcus, and oxidative stress. We discovered that mucosal metabolites supported general growth of ileal E. coli, with a selective effect of ethanolamine on AIEC that was augmented by cometabolism of ileitis-associated amino acids and glutathione and by symbiosis-associated fucose. This metabolic plasticity was facilitated by the eut and pdu microcompartments, amino acid metabolism, γ-glutamyl-cycle, and pleiotropic stress responses. We linked metabolism to virulence and found that ethanolamine and glutamine enhanced AIEC motility, infectivity, and proinflammatory responses in vitro. We connected use of ethanolamine to intestinal inflammation and L-fuculose phosphate aldolase (fucA) to symbiosis in AIEC monoassociated IL10–/– mice. Collectively, we established that AIEC were pathoadapted to utilize mucosal metabolites associated with health and inflammation for growth and virulence, enabling the transition from symbiont to pathogen in a susceptible host.
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Affiliation(s)
- Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Francois-Pierre Martin
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Susan R Strickler
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Akihiko Oka
- Department of Internal Medicine II, Shimane University Faculty of Medicine, Izumo, Japan
| | - Jeremy Herzog
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Bo Liu
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Scot E Dowd
- MR DNA: Molecular Research LP, Shallowater, United States of America
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | | | - Esra I Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Rhonda Yantiss
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Lukas A Mueller
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - R Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
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50
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Davies M, Galazzo G, van Hattem JM, Arcilla MS, Melles DC, de Jong MD, Schultsz C, Wolffs P, McNally A, van Schaik W, Penders J. Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli. Gut Microbes 2022; 14:2060676. [PMID: 35388735 PMCID: PMC8993065 DOI: 10.1080/19490976.2022.2060676] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Previous studies have shown high acquisition risks of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among international travelers visiting antimicrobial resistance (AMR) hotspots. Although antibiotic use and travelers' diarrhea have shown to influence the ESBL-E acquisition risk, it remains largely unknown whether successful colonization of ESBL-E during travel is associated with the composition, functional capacity and resilience of the traveler's microbiome. The microbiome of pre- and post-travel fecal samples from 190 international travelers visiting Africa or Asia was profiled using whole metagenome shotgun sequencing. A metagenomics species concept approach was used to determine the microbial composition, population diversity and functional capacity before travel and how it is altered longitudinally. Eleven travelers were positive for ESBL-E before travel and removed from the analysis. Neither the microbial richness (Chao1), diversity (effective Shannon) and community structure (Bray-Curtis dissimilarity) in pretravel samples nor the longitudinal change of these metrics during travel were predictive for ESBL-E acquisition. A zero-inflated two-step beta-regression model was used to determine how the longitudinal change in both prevalence and abundance of each taxon was related to ESBL acquisition. There were detected increases in both the prevalence and abundance of Citrobacter freundii and two members of the genus Bacteroides, in association with remaining uncolonized by ESBL-E. These results highlight the potential of these individual microbes as a microbial consortium to prevent the acquisition of ESBL-E. The ability to alter a person's colonization resistance to a bacterium could be key to intervention strategies that aim to minimize the spread of MDR bacteria.
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Affiliation(s)
- Matthew Davies
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK,Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Gianluca Galazzo
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Jarne M. van Hattem
- Department of Medical Microbiology, Amsterdam University Medical Center, AMC, Amsterdam, The Netherlands
| | - Maris S. Arcilla
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Damian C. Melles
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Menno D. de Jong
- Department of Medical Microbiology, Amsterdam University Medical Center, AMC, Amsterdam, The Netherlands
| | - Constance Schultsz
- Department of Medical Microbiology, Amsterdam University Medical Center, AMC, Amsterdam, The Netherlands,Department of Global Health, Amsterdam Institute for Global Health and Development, AMC, Amsterdam, The Netherlands
| | - Petra Wolffs
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - John Penders
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands,Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands,CONTACT John Penders Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
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